1 OVERVIEW

Question this study addresses:

NOTE: THE ANALYSES CONTAINED HEREIN WILL BE FOR A MANUSCRIPT BASED ON APS 2017.
ADDITIONAL ANALYSES AND RESULTS FOR THE POSTER WILL BE IN A DIFFERENT FILE.

FIX THE TEXT BELOW

1.1 ABSTRACT

1.1.1 Title

Significant differences in sleep and depression among chronic pain groups: Implications for patient education

1.1.2 Purpose

2 START

3 DATA

Import data from GitHub

Import Subs list from GitHub

subs <- read.csv(url('https://raw.githubusercontent.com/BrainStormCenter/Manuscripts/master/Mood_DMN_2gps/SubjectList_2020_12_11_v1.csv'), header = TRUE)
subs <- as_tibble(subs)
subs <- subs %>% dplyr::select("ID") # has imaging data

3.1 Subset

# A tibble: 5 x 2
  group     n
  <int> <int>
1     0     1
2     1    53
3     2    80
4     3    52
5    NA     1
# A tibble: 3 x 2
  group.factor     n
  <fct>        <int>
1 HC              35
2 CLBP            63
3 FM              25

3.2 PSQI

  • The global PSQI score is then calculated by totaling the seven component scores, providing an overall score ranging from 0 to 21, where lower scores denote a healthier sleep quality.

  • A PSQI Global score ≥ 5 is the clinical cutoff score (i.e., sleep problems)

  • The PSQI data has been updated, processed, clean and scored

  • NOTE: I need to add a section that discusses the PSQI cutoff. Anything over “5” is considered significant.

3.3 INITIAL DATA SETS

Create a small dataset (dat.sm) that includes only the variables of interest.

3.4 VARIANCE CHECK

Which variable(s) in the dat.sm data has potential issues with variances?

[1] "slpDist"

4 SAMPLE DESCRIPTIVES

Group by sex for overall sample.
Entire Sample
Sex
Group Female Male Total
HC 21 14 35
CLBP 40 23 63
FM 22 3 25
Total 83 40 123

Means and SDs for each group.


 Descriptive statistics by group 
group: HC
              vars  n mean   sd   se
group.factor*    1 35 1.00 0.00 0.00
slpQual          2 35 0.77 0.65 0.11
slpLat           3 35 0.86 0.77 0.13
slpDur           4 35 0.69 0.72 0.12
slpEff           5 35 1.20 1.37 0.23
slpDayFcn        6 35 0.26 0.44 0.07
psqi_Global      7 35 5.03 2.98 0.50
ess_total        8 35 6.09 2.73 0.46
bdi_total        9 35 3.11 4.08 0.69
mcgill_total    10 35 2.14 7.35 1.24
------------------------------------------------------------ 
group: CLBP
              vars  n  mean    sd   se
group.factor*    1 63  2.00  0.00 0.00
slpQual          2 63  1.21  0.79 0.10
slpLat           3 63  1.25  0.80 0.10
slpDur           4 63  0.86  0.72 0.09
slpEff           5 63  1.35  1.31 0.16
slpDayFcn        6 63  0.22  0.42 0.05
psqi_Global      7 63  6.46  2.85 0.36
ess_total        8 63  6.84  3.50 0.44
bdi_total        9 63  9.63  7.72 0.97
mcgill_total    10 63 24.83 15.03 1.89
------------------------------------------------------------ 
group: FM
              vars  n  mean    sd   se
group.factor*    1 25  3.00  0.00 0.00
slpQual          2 25  1.76  0.72 0.14
slpLat           3 25  2.28  0.98 0.20
slpDur           4 25  1.52  0.96 0.19
slpEff           5 25  1.72  1.31 0.26
slpDayFcn        6 25  0.08  0.28 0.06
psqi_Global      7 25  9.88  3.64 0.73
ess_total        8 25  7.28  3.94 0.79
bdi_total        9 25 15.40  9.11 1.82
mcgill_total    10 25 35.16 13.60 2.72
------------------------------------------------------------ 
group: TRUE
NULL

#PLOTS

4.1 CORR PLOTS

The end of corr plots

4.2 BAR PLOTS

4.3 BOX PLOTS

5 ANOVA (Main effect of group)

ANOVA full model
Name p.value
slpQual 6.8e-06
slpLat 6.61e-09
slpDur 0.000173
slpEff 0.317
slpDist 0.287
slpMeds 2.04e-05
slpDayFcn 0.215
psqi_Global 7.29e-08
ess_total 0.374
isi_total 0.000299
bdi_total 9.01e-09
mcgill_total 1.61e-17
TIB 0.995
Note:
Red = Significant main effect for group (p ≤ 0.05)

5.1 POSTHOC

PostHoc group comparisons: See Note at table end
contrast null.value diff conf.low conf.high adj.p.value
Sleep Quality
CLBP-HC 0.000 0.435 0.067 0.803 0.0162
FM-HC 0.000 0.989 0.531 1.446 3.4e-06
FM-CLBP 0.000 0.554 0.141 0.967 0.00527
Sleep Latency
CLBP-HC 0.000 0.397 -0.020 0.814 0.0656
FM-HC 0.000 1.423 0.905 1.940 5.14e-09
FM-CLBP 0.000 1.026 0.559 1.493 2.36e-06
Sleep Duration
CLBP-HC 0.000 0.171 -0.215 0.558 0.545
FM-HC 0.000 0.834 0.355 1.314 0.0002
FM-CLBP 0.000 0.663 0.230 1.096 0.0012
Sleep Efficacy
CLBP-HC 0.000 0.149 -0.514 0.813 0.855
FM-HC 0.000 0.520 -0.304 1.344 0.296
FM-CLBP 0.000 0.371 -0.373 1.115 0.466
Sleep Disturbance
CLBP-HC 0.000 0.029 -0.016 0.074 0.292
FM-HC 0.000 0.029 -0.027 0.084 0.448
FM-CLBP 0.000 0.000 -0.050 0.050 1
Sleep Medications
CLBP-HC 0.000 0.286 -0.216 0.788 0.37
FM-HC 0.000 1.234 0.611 1.858 2.1e-05
FM-CLBP 0.000 0.949 0.386 1.511 0.000323
Sleep Daytime Functioning
CLBP-HC 0.000 -0.035 -0.236 0.166 0.911
FM-HC 0.000 -0.177 -0.427 0.073 0.216
FM-CLBP 0.000 -0.142 -0.368 0.083 0.297
PSQI Global
CLBP-HC 0.000 1.432 -0.099 2.962 0.0719
FM-HC 0.000 4.851 2.950 6.753 4.94e-08
FM-CLBP 0.000 3.420 1.703 5.136 1.85e-05
ESS Total
CLBP-HC 0.000 0.756 -0.944 2.455 0.544
FM-HC 0.000 1.194 -0.916 3.305 0.374
FM-CLBP 0.000 0.439 -1.466 2.344 0.848
ISI Total
CLBP-HC 0.000 4.333 -1.885 10.552 0.223
FM-HC 0.000 9.619 3.171 16.067 0.00198
FM-CLBP 0.000 5.286 1.668 8.903 0.00247
BDI Total
CLBP-HC 0.000 6.521 2.909 10.132 0.000109
FM-HC 0.000 12.286 7.800 16.771 5.76e-09
FM-CLBP 0.000 5.765 1.716 9.814 0.0028
McGill Total
CLBP-HC 0.000 22.683 16.179 29.186 6.59e-13
FM-HC 0.000 33.017 24.940 41.095 5.14e-14
FM-CLBP 0.000 10.335 3.043 17.626 0.00295
Time in Bed
CLBP-HC 0.000 0.228 -5.369 5.825 0.995
FM-HC 0.000 0.243 -6.709 7.194 0.996
FM-CLBP 0.000 0.015 -6.260 6.290 1
Note:
Red = Significant group tests (p ≤ 0.05)

STOP HERE

6 ISI ANALYSES

This set of analyses uses a subset of subjects who have completed the ISI

Also create a dataset of subjects with ISI data (dat.isi).

6.1 ISI DATA VARIANCE

The variable(s) in the ISI data with variance issues are:

7 END - BEYOND HERE IS EXPLORATORY